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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ), 'gf_id' => 'HOM05D001311', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001311' ), 'data_identifier' => 'HOM05D001311', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001311', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33920' => 'bna', 'A04p24690' => 'bna', 'A04p24700' => 'bna', 'A05p13470' => 'bna', 'A05p13500' => 'bna', 'A05p26090' => 'bna', 'Aa31LG5G15330' => 'aar', 'Aa31LG5G4980' => 'aar', 'Aa31LG5G4990' => 'aar', 'Actinidia08484' => 'ach', 'Actinidia23524' => 'ach', 'Actinidia36951' => 'ach', 'Ah.07g206890' => 'amhyb', 'Ah.13g068800' => 'amhyb', 'AL3G15260' => 'aly', 'AL3G36880' => 'aly', 'AL4G27400' => 'aly', 'AL4G27410' => 'aly', 'Aqoxy2G01171' => 'aox', 'Aqoxy2G01172' => 'aox', 'Aqoxy2G01729' => 'aox', 'Aqoxy2G03414' => 'aox', 'Aqoxy2G03415' => 'aox', 'Aqoxy2G03416' => 'aox', 'Aqoxy2G03417' => 'aox', 'Aqoxy2G03418' => 'aox', 'Aqoxy4G00823' => 'aox', 'Aqoxy5G00435' => 'aox', 'Aqoxy5G00436' => 'aox', 'Aqoxy7G03220' => 'aox', 'arahy.Tifrunner.gnm1.ann1.240KDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.415TK8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2PPBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F82WRM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ML1PU9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1JLUS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QRU6X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6WHGD' => 'arhy', 'AT2G32020' => 'ath', 'AT2G32030' => 'ath', 'AT3G22560' => 'ath', 'Atru.chr2.658' => 'acertr', 'Atru.chr2.659' => 'acertr', 'Atru.chr2.660' => 'acertr', 'Atru.chr4.2440' => 'acertr', 'Atru.chr4.2441' => 'acertr', 'Atru.chr4.2442' => 'acertr', 'Atru.chr4.2443' => 'acertr', 'Atru.ctg752_3.56' => 'acertr', 'Atru.ctg752_3.57' => 'acertr', 'Atru.ctg752_3.58' => 'acertr', 'AUR62000957' => 'cqu', 'AUR62005011' => 'cqu', 'AUR62015949' => 'cqu', 'AUR62015950' => 'cqu', 'AUR62018402' => 'cqu', 'AUR62021041' => 'cqu', 'AUR62021156' => 'cqu', 'BcaB02g10440' => 'bca', 'BcaB04g19288' => 'bca', 'BcaB04g20511' => 'bca', 'BcaB04g20512' => 'bca', 'BcaB06g26370' => 'bca', 'BcaB06g28580' => 'bca', 'BcaB06g28581' => 'bca', 'BcaC01g04342' => 'bca', 'BcaC02g07925' => 'bca', 'BcaC02g07950' => 'bca', 'BcaC02g07951' => 'bca', 'BcaC05g28035' => 'bca', 'BcaC09g49181' => 'bca', 'BolC1t04128H' => 'bol', 'BolC3t16412H' => 'bol', 'BolC4t23306H' => 'bol', 'BolC4t27647H' => 'bol', 'BolC4t27648H' => 'bol', 'BolC5t32793H' => 'bol', 'BraA03t12567Z' => 'bra', 'BraA04t17988Z' => 'bra', 'BraA04t17989Z' => 'bra', 'BraA05t20283Z' => 'bra', 'BraA05t20286Z' => 'bra', 'BraA05t21492Z' => 'bra', 'C03p41300' => 'bna', 'C04p17590' => 'bna', 'C04p61630' => 'bna', 'C04p61640' => 'bna', 'C04p61890' => 'bna', 'C05p40530' => 'bna', 'CAN.G1094.15' => 'can', 'CAN.G1094.16' => 'can', 'CAN.G1094.18' => 'can', 'CAN.G1094.19' => 'can', 'CAN.G134.180' => 'can', 'CAN.G134.182' => 'can', 'CAN.G134.183' => 'can', 'CAN.G134.184' => 'can', 'CAN.G231.7' => 'can', 'CAN.G630.59' => 'can', 'CANSAT54G0524' => 'cansat', 'CANSAT54G2726' => 'cansat', 'CANSAT78G1189' => 'cansat', 'CANSAT78G2240' => 'cansat', 'CANSAT78G2342' => 'cansat', 'CARHR079230' => 'chi', 'CARHR079240' => 'chi', 'CARHR098460' => 'chi', 'CARHR098470' => 'chi', 'CARHR125810' => 'chi', 'CARHR125820' => 'chi', 'Carub.0003s0416' => 'cru', 'Carub.0003s2273' => 'cru', 'Carub.0004s1337' => 'cru', 'Carub.0004s1338' => 'cru', 'Ca_09398_v3' => 'car', 'Ca_24405_v3' => 'car', 'Ca_24406_v3' => 'car', 'Ca_30168_v3' => 'car', 'Cc02_g31320' => 'ccan', 'Cc03_g03980' => 'ccan', 'Cc03_g03990' => 'ccan', 'Cc03_g04000' => 'ccan', 'Ciclev10002694m.g' => 'ccl', 'Ciclev10003433m.g' => 'ccl', 'Ciclev10005971m.g' => 'ccl', 'Ciclev10005998m.g' => 'ccl', 'Ciclev10005999m.g' => 'ccl', 'Ciclev10006418m.g' => 'ccl', 'Ciclev10009635m.g' => 'ccl', 'Ciclev10029795m.g' => 'ccl', 'CiPaw.01G168100' => 'cil', 'CiPaw.01G168200' => 'cil', 'CiPaw.02G098800' => 'cil', 'CiPaw.07G008400' => 'cil', 'CiPaw.08G178200' => 'cil', 'ClCG03G016320' => 'cla', 'COL.COLO4_15252' => 'col', 'COL.COLO4_21498' => 'col', 'COL.COLO4_21500' => 'col', 'COL.COLO4_21502' => 'col', 'COL.COLO4_21503' => 'col', 'COL.COLO4_21504' => 'col', 'COL.COLO4_21505' => 'col', 'COL.COLO4_21506' => 'col', 'COL.COLO4_21507' => 'col', 'COL.COLO4_21508' => 'col', 'COL.COLO4_21510' => 'col', 'Cpa.g.sc1119.1' => 'cpa', 'Cpa.g.sc117.41' => 'cpa', 'Cpa.g.sc58.87' => 'cpa', 'Cpa.g.sc58.88' => 'cpa', 'CsaV3_1G039640' => 'csa', 'CsaV3_3G013140' => 'csa', 'CsaV3_3G013150' => 'csa', 'CSS0004976' => 'camsi', 'CSS0008296' => 'camsi', 'CSS0018712' => 'camsi', 'CSS0022770' => 'camsi', 'CSS0026047' => 'camsi', 'CSS0028312' => 'camsi', 'CSS0028439' => 'camsi', 'DCAR_002377' => 'dca', 'DCAR_002378' => 'dca', 'DCAR_017899' => 'dca', 'DCAR_030648' => 'dca', 'DCAR_030649' => 'dca', 'DCAR_030651' => 'dca', 'DCAR_030652' => 'dca', 'Dinv14008' => 'din', 'Dinv17740' => 'din', 'Dinv44549' => 'din', 'Dinv44550' => 'din', 'Duzib151G0044' => 'dzi', 'Duzib151G0208' => 'dzi', 'Duzib151G0685' => 'dzi', 'Duzib177G0881' => 'dzi', 'ECA246G4164' => 'eca', 'EL10Ac3g07291' => 'bvu', 'EL10Ac4g09203' => 'bvu', 'Eucgr.B01057' => 'egr', 'Eucgr.H03444' => 'egr', 'Eucgr.H03445' => 'egr', 'Eucgr.H03446' => 'egr', 'Eucgr.H03449' => 'egr', 'Eucgr.H04392' => 'egr', 'FAN05G3625' => 'fan', 'FAN05G3956' => 'fan', 'FAN07G0075' => 'fan', 'FAN07G1835' => 'fan', 'FAN09G2018' => 'fan', 'FAN09G2892' => 'fan', 'FAN12G0418' => 'fan', 'FAN12G0736' => 'fan', 'FAN12G1141' => 'fan', 'FAN12G1914' => 'fan', 'FAN14G4548' => 'fan', 'FAN19G2816' => 'fan', 'FAN24G2919' => 'fan', 'FAN27G1125' => 'fan', 'FvH4_2g12711' => 'fve', 'FvH4_4g16130' => 'fve', 'FvH4_4g16140' => 'fve', 'FvH4_4g26600' => 'fve', 'FvH4_4g26610' => 'fve', 'FvH4_6g03890' => 'fve', 'Glyma.01G236500' => 'gma', 'Glyma.01G236700' => 'gma', 'Glyma.10G245300' => 'gma', 'Glyma.18G290000' => 'gma', 'Glyma.19G241500' => 'gma', 'Glyma.19G241600' => 'gma', 'Gohir.A02G033500' => 'ghi', 'Gohir.A02G033501' => 'ghi', 'Gohir.A13G106032' => 'ghi', 'Gohir.D02G040000' => 'ghi', 'Gohir.D02G040100' => 'ghi', 'Gohir.D09G213300' => 'ghi', 'Gohir.D13G108800' => 'ghi', 'Gorai.005G044300' => 'gra', 'Gorai.005G044500' => 'gra', 'Gorai.006G233400' => 'gra', 'Gorai.013G122300' => 'gra', 'GSVIVG01018002001' => 'vvi', 'GSVIVG01018003001' => 'vvi', 'GSVIVG01018005001' => 'vvi', 'GSVIVG01021886001' => 'vvi', 'HanXRQChr16g0512001' => 'han', 'Haze_00871' => 'cav', 'Haze_00878' => 'cav', 'Haze_00879' => 'cav', 'Hma1.2p1_0602F.1_g187470' => 'hma', 'Hma1.2p1_1572F.1_g291340' => 'hma', 'Hma1.2p1_1572F.1_g291360' => 'hma', 'Hma1.2p1_2201F.1_g317010' => 'hma', 'Hma1.2p1_2201F.1_g317020' => 'hma', 'HPP92_012121' => 'vpl', 'HPP92_012129' => 'vpl', 'HPP92_017653' => 'vpl', 'Hund12112' => 'sun', 'Hund19070' => 'sun', 'Lalb_Chr09g0319901' => 'lal', 'Lalb_Chr09g0319921' => 'lal', 'Lalb_Chr15g0076951' => 'lal', 'Lj1g0007580' => 'lja', 'LjContig00408g0015666' => 'lja', 'LjContig00408g0027005' => 'lja', 'Manes.03G176700' => 'mes', 'Manes.03G176800' => 'mes', 'Manes.15G030201' => 'mes', 'Manes.15G030300' => 'mes', 'MBI04_g13669_MAGBIO' => 'mbi', 'MBI05_g12087_MAGBIO' => 'mbi', 'MBI16_g26395_MAGBIO' => 'mbi', 'MD04G1217600' => 'mdo', 'MD12G1234400' => 'mdo', 'MD12G1234600' => 'mdo', 'MD12G1234800' => 'mdo', 'MD13G1195500' => 'mdo', 'MD13G1195600' => 'mdo', 'MD16G1196300' => 'mdo', 'MD16G1196400' => 'mdo', 'MD16G1196500' => 'mdo', 'Medtr1g103110' => 'mtr', 'Medtr1g103150' => 'mtr', 'Medtr1g103320' => 'mtr', 'Medtr3g463610' => 'mtr', 'Medtr5g006450' => 'mtr', 'Medtr5g006460' => 'mtr', 'Medtr5g006470' => 'mtr', 'Medtr5g006510' => 'mtr', 'Medtr7g024760' => 'mtr', 'Medtr7g024765' => 'mtr', 'Medtr7g024780' => 'mtr', 'Medtr7g114410' => 'mtr', 'MELO3C006521.2' => 'cme', 'MELO3C006522.2' => 'cme', 'MELO3C015386.2' => 'cme', 'Migut.G00351' => 'egut', 'Migut.G00352' => 'egut', 'Migut.G00353' => 'egut', 'Migut.N00445' => 'egut', 'Migut.N00446' => 'egut', 'Migut.N00447' => 'egut', 'Migut.N00448' => 'egut', 'MSTRG.9972' => 'ama', 'Nitab4.5_0000321g0130' => 'nta', 'Nitab4.5_0001157g0010' => 'nta', 'Nitab4.5_0001157g0020' => 'nta', 'Nitab4.5_0001237g0010' => 'nta', 'Nitab4.5_0001237g0020' => 'nta', 'Nitab4.5_0001237g0030' => 'nta', 'Nitab4.5_0001834g0040' => 'nta', 'Nitab4.5_0002361g0220' => 'nta', 'Nitab4.5_0002840g0150' => 'nta', 'Nitab4.5_0006783g0010' => 'nta', 'Nitab4.5_0007068g0030' => 'nta', 'Nitab4.5_0007400g0020' => 'nta', 'Nitab4.5_0012606g0010' => 'nta', 'Nn1g02361' => 'nnu', 'Nn1g02362' => 'nnu', 'Nn3g21365' => 'nnu', 'Nn5g27734' => 'nnu', 'Nn5g27735' => 'nnu', 'Nn6g34099' => 'nnu', 'Nn6g34100' => 'nnu', 'Nn6g34102' => 'nnu', 'Nn6g34103' => 'nnu', 'Nn6g34104' => 'nnu', 'Oeu049781.1' => 'oeu', 'Oeu049782.1' => 'oeu', 'Oeu063498.1' => 'oeu', 'Os01g0358800' => 'osa', 'Os03g0664800' => 'osa', 'Os03g0665000' => 'osa', 'Os03g0794200' => 'osa', 'Os03g0794300' => 'osa', 'Os03g0794400' => 'osa', 'Os04g0259100' => 'osa', 'Peaxi162Scf00092g00043' => 'pax', 'Peaxi162Scf00092g00414' => 'pax', 'Peaxi162Scf00131g00129' => 'pax', 'Peaxi162Scf00225g00116' => 'pax', 'Peaxi162Scf00225g00122' => 'pax', 'Peaxi162Scf00225g00131' => 'pax', 'Peaxi162Scf00225g00132' => 'pax', 'PGR004G0747' => 'pgr', 'PGR004G0929' => 'pgr', 'PGR004G1722' => 'pgr', 'PGR044G0920' => 'pgr', 'PGSC0003DMG400006337' => 'stu', 'PGSC0003DMG400022467' => 'stu', 'PGSC0003DMG400022468' => 'stu', 'PGSC0003DMG400022469' => 'stu', 'PGSC0003DMG400027730' => 'stu', 'PGSC0003DMG400032271' => 'stu', 'PGSC0003DMG400032272' => 'stu', 'PGSC0003DMG400032273' => 'stu', 'PGSC0003DMG400038970' => 'stu', 'Phvul.002G044100' => 'pvu', 'Phvul.006G098000' => 'pvu', 'Potri.007G102900' => 'ptr', 'Potri.008G154700' => 'ptr', 'Potri.008G154800' => 'ptr', 'Potri.010G085600' => 'ptr', 'Pp3c13_24240' => 'ppa', 'Pp3c16_22100' => 'ppa', 'Pp3s405_20' => 'ppa', 'Prupe.1G016400' => 'ppe', 'Prupe.1G016500' => 'ppe', 'Prupe.1G016600' => 'ppe', 'Prupe.1G016700' => 'ppe', 'Prupe.6G337400' => 'ppe', 'Psat0s477g0040' => 'psa', 'Psat0s477g0080' => 'psa', 'Psat4g209680' => 'psa', 'Psat4g209720' => 'psa', 'Psat4g209840' => 'psa', 'Psat6g205840' => 'psa', 'PSO170G3182' => 'pso', 'PSO210G2080' => 'pso', 'PSO210G3021' => 'pso', 'PSO761G0572' => 'pso', 'QL03p000264' => 'qlo', 'QL06p001881' => 'qlo', 'QL06p001940' => 'qlo', 'QL06p001948' => 'qlo', 'QL06p001953' => 'qlo', 'QL06p001965' => 'qlo', 'RcHm_v2.0_Chr3g0452461' => 'rch', 'RcHm_v2.0_Chr4g0415651' => 'rch', 'RcHm_v2.0_Chr4g0415661' => 'rch', 'RcHm_v2.0_Chr4g0415671' => 'rch', 'RcHm_v2.0_Chr4g0415681' => 'rch', 'RcHm_v2.0_Chr4g0415691' => 'rch', 'RcHm_v2.0_Chr4g0415701' => 'rch', 'RcHm_v2.0_Chr4g0415711' => 'rch', 'RcHm_v2.0_Chr6g0273471' => 'rch', 'Rhsim02G0026400' => 'rsi', 'Rhsim02G0026500' => 'rsi', 'Rhsim02G0026600' => 'rsi', 'Rhsim04G0201000' => 'rsi', 'Rhsim04G0201100' => 'rsi', 'Rhsim04G0201200' => 'rsi', 'Rhsim05G0149900' => 'rsi', 'RhsimUnG0025600' => 'rsi', 'RhsimUnG0028600' => 'rsi', 'RhsimUnG0028700' => 'rsi', 'Sabra10G0058000' => 'sbr', 'SalBow2G0353' => 'sbo', 'SalBow2G0663' => 'sbo', 'SalBow2G1348' => 'sbo', 'Sc06g0003600' => 'sci', 'Sc06g0003610' => 'sci', 'Sc06g0003620' => 'sci', 'Sc13g0004510' => 'sci', 'Sc13g0006060' => 'sci', 'Sc19g0004050' => 'sci', 'Sed0001668' => 'sed', 'Sed0008152' => 'sed', 'Sed0012209' => 'sed', 'Sed0017251' => 'sed', 'SEGI_00649' => 'sgi', 'SEGI_14958' => 'sgi', 'SEGI_15707' => 'sgi', 'SEGI_24651' => 'sgi', 'SEGI_27613' => 'sgi', 'SEGI_34772' => 'sgi', 'SEGI_35109' => 'sgi', 'SEGI_36401' => 'sgi', 'SGA_v2.0_scaffold191G40509' => 'sas', 'SMO118G0529' => 'smo', 'Solyc01g097990.3' => 'sly', 'Solyc01g098010.4' => 'sly', 'Solyc01g098020.2' => 'sly', 'Solyc06g054090.2' => 'sly', 'Solyc09g082220.1' => 'sly', 'Solyc09g082230.1' => 'sly', 'Solyc09g082250.3' => 'sly', 'Solyc09g082260.1' => 'sly', 'Sopen01g041570' => 'spe', 'Sopen01g041580' => 'spe', 'Sopen01g041590' => 'spe', 'Sopen06g019250' => 'spe', 'Sopen09g031100' => 'spe', 'Sopen09g031110' => 'spe', 'Sopen09g031120' => 'spe', 'Sopen09g031130' => 'spe', 'Sopen09g031140' => 'spe', 'Sp3g20340' => 'spa', 'Sp3g20350' => 'spa', 'Sp4g14430' => 'spa', 'Sp4g14440' => 'spa', 'Sp4g14450' => 'spa', 'TAR365G0100' => 'tar', 'TAR365G0934' => 'tar', 'TAR365G1051' => 'tar', 'TAR627G0599' => 'tar', 'TAR636G0293' => 'tar', 'TAR636G0806' => 'tar', 'TAR636G3534' => 'tar', 'THA.LOC104815883' => 'tha', 'THA.LOC104818651' => 'tha', 'Thecc.04G234300' => 'tca', 'Thecc.04G234500' => 'tca', 'Thecc.05G291100' => 'tca', 'Thhalv10017278m.g' => 'esa', 'Thhalv10017288m.g' => 'esa', 'Thhalv10021594m.g' => 'esa', 'Thhalv10022340m.g' => 'esa', 'TPR.G16179' => 'tpr', 'TPR.G16183' => 'tpr', 'TPR.G20347' => 'tpr', 'TPR.G20382' => 'tpr', 'TPR.G26082' => 'tpr', 'TPR.G27104' => 'tpr', 'TPR.G28326' => 'tpr', 'TPR.G36021' => 'tpr', 'TPR.G37957' => 'tpr', 'TPR.G6936' => 'tpr', 'TWI09G0509' => 'twi', 'TWI12G0002' => 'twi', 'TWI34G1927' => 'twi', 'TWI53G0313' => 'twi', 'TWI53G0321' => 'twi', 'TWI53G0858' => 'twi', 'vmacro15353' => 'vma', 'VMungo0540G0914' => 'vmu', 'VMungo1215G0878' => 'vmu', 'VMungo1215G3166' => 'vmu', 'Zm00001eb060500' => 'zma', 'Zm00001eb060510' => 'zma', 'Zm00001eb060530' => 'zma', 'Zm00001eb086010' => 'zma', 'Zm00001eb090110' => 'zma', 'Zm00001eb090120' => 'zma', 'Zm00001eb090130' => 'zma', 'Zm00001eb161090' => 'zma', 'Zm00001eb213090' => 'zma', 'Zm00001eb217870' => 'zma' ) $gf_id = 'HOM05D001311' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001311' ) $data_identifier = 'HOM05D001311' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 12, 'arhy' => (int) 8, 'ath' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 11, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 3, 'lja' => (int) 3, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 9, 'mtr' => (int) 12, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 1, 'nta' => (int) 13, 'nnu' => (int) 10, 'oeu' => (int) 3, 'osa' => (int) 7, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 9, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 9, 'rsi' => (int) 10, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 8, 'sas' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 10, 'twi' => (int) 6, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb217870' $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